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ABI 102 WINTER QTR > Midterm 2 > Flashcards

Midterm 2 Flashcards

1
Q

How many carbons do monosaccharides range between?

A

3 to 8 carbons

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2
Q

Most common number of carbons in monosaccharides?

A

Hexoses - 6 carbons
Pentoses - 5 carbons

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3
Q

What is an Aldose?

A

Carbonyl at the end of the carbon chain

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4
Q

What is a Ketose?

A

Carbonyl at any location or elsewhere

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5
Q

What are chiral centers?

A

Carbons with four different substituents

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6
Q

What do chiral centers partly determine?

A

the type of monossacharide

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7
Q

What are the two types of chiral centers?

A

Epimers
Enantiomers

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8
Q

What are Epimers?

A

Monosaccharides that only differ in configuration at one chiral center

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9
Q

What are examples of Epimers?

A

glucose and mannose

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10
Q

What are Enantiomers?

A

Monosaccharides that differ in configurations at all chiral centers

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11
Q

What are examples of Enantiomers?

A

D- and L- glucose

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12
Q

Most carbohydrates in living organisms are _____________.

A

D- isomers

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13
Q

What structure do most monosaccharides have?

A

Cyclical structure

— ≥ 4 Carbons have cyclical structure
— they are not written as straight chains

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14
Q

In monosaccharides, what are the two forms of anomers

A

ß anomer (beta)
∂ anomer (alpha)

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15
Q

What are ß anomers?

A

-OH of anomeric carbonyl C up
- same side as C-6

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16
Q

What are ∂ anomers?

A

-OH of anomeric carbonyl D down
- Opposite side from C-6

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17
Q

Why learn about ∂ vs. ß anomers?

A

Anomeric configuration determines structural properties.
—— Example:
- Starch (good for eating) = contains ∂- glucose
- Cellulose (good for wearing) = contains ß - glucose

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18
Q

What is Pyranose?

A

5 carbons + 1 oxygen ring

Example: glucopyranose (glucose)

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19
Q

What is Furanose?

A

4 carbons + 1 oxygen in ring

Example: fructofuranose (fructose)

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20
Q

What structure do most monosaccharides have?

A

Cyclical structure

— ≥ 4 Carbons have a cyclical structure
— they are not written as straight chains

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21
Q

Since some monosaccharides are reducing sugars, What are reducing sugars?

A
  • Easily reduce copper ions and other compounds
    - Sugar is itself oxidized during the process
  • The site of oxidation is the anomeric carbon (carbonyl)
    - Oxizided to carboxyl
    + Example: glucose (carbon 1)
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22
Q

Why are reducing sugars introduced or important?

A
  • They are important for detecting sugars + historically in detecting diabetes.
    • in detecting sugars, an oxidizing agent that turns color when reduced
    • Common agent: 3,5 dinitrosalicylic agent (easy way to detect glucose in the sample)

— old way of detecting diabetes would be Drs. tasting urine

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23
Q

Monosaccharides have many derivatives, what are the four derivatives talked about in class?

A
  1. Amino Sugars (-OH to -NH2)
  2. Deoxy Sugars (-OH to -H)
  3. Acidic Sugars (-CH2OH to -COO-)
  4. Sugar Phosphates (-OH to -OPO3^2-)
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24
Q

What are the building blocks for more complex carbohydrates?

A

Monosaccharides

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25
Q

Simple Sugar

A

Monosaccharide

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26
Q

2 Monosaccharides

A

Disaccharides

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27
Q

Oligosaccharides

A

3 to ~9 monosaccharides

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28
Q

Many monosaccharides (~10 or more)

A

Polysaccharides

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29
Q

How are Disaccharides formed?

A

Formed when anomeric carbon of one monosaccharide is linked with another monosaccharide

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30
Q

What is the linkage called in forming a disaccharide?

A

glycosidic bond

Example: condensation reaction (forming water)

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31
Q

What are the Common Disaccharides?

A
  • Maltose (from starch)
  • Lactose (from milk sugar)
  • Sucrose (from photosynthesis) - storage in plants
  • Cellobiose (from cellulose)
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32
Q

How are glycosidic bonds named?

A
  • position of carbons involved
  • anomeric configuration of the carbons

Example: Glc (∂1–>4) Glc

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33
Q

What is the glycosidic bond of Maltose

A

Glc (∂1–>4) Glcq

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34
Q

What is the glycosidic bond of Cellobiose?

A

Glc (ß1–>4) Glc

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35
Q

What is the glycosidic bond of Sucrose?

A

Glc (∂1 <–>ß2) Fru

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36
Q

What is the glycosidic bond of Lactose?

A

Gal (ß 1—> 4) Glc

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37
Q

What kind of arrow would it be if there are 2 anomeric carbons?

A

<––>

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38
Q

What kind of arrow would it be if there is 1 anomeric carbon?

A

––>

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39
Q

What is a reducing end?

A
  • End of a disaccharide with a free anomeric carbon
  • Detectable with DNS or oxidizing agent
  • It is not present in all disaccharides
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40
Q

What is an example of a reducing end?

A

Sucrose
- Resistance to oxidation makes sucrose good storage compound in plants

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41
Q

Why are polysaccharides important biomolecules?

A

Location of most carbohydrates in organisms

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42
Q

What is the most abundant biomolecule on Earth?

A

Cellulose

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43
Q

What is the second most abundant biomolecule on Earth?

A

Chitin

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44
Q

Since polysaccharides take on many forms, What are the structural classes?

A
  • Homopolysaccharides
  • Heteropolysaccharides
  • Branched
  • Unbranched
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45
Q

What type of structural class of polysaccharide is made out of single monosaccharides?

  • Simplest and made out of a straight chain
A

Homopolysaccharides

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46
Q

What type of structural class of polysaccharide is made out of different monosaccharides?

A

Heteropolysaccharides

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47
Q

What type of structural class of polysaccharide is made out of single monosaccharides?

A

Homopolysaccharides

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48
Q

What type of structural class of polysaccharide is made out of either homo/hetero-polysaccharides that are branched?

A

Branched

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49
Q

What type of structural class of polysaccharide is made out of either homo/hetero-polysaccharides that are in a straight chain?

A

Unbranched

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50
Q

What are examples of polysaccharides that are used for storage?

A
  • Starch, Glycogen and Fructan
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51
Q

What are the two components of starch?

A

Amylose - unbranched Glc(∂1–>4) Glc
(homopolysaccharides)

Amylopectin - Glc(∂1–>6) Glc branches every 24 to 30 residues
- similar to amylose
-branched polysaccharide

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52
Q

What is Corn Starch made out of?

A

24% amylose and 76% amylopectin

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53
Q

Where is starch found?

A

Found in plant endosperm

– seed tissue containing starch granules in grains
– protein matrix surround starch granule

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54
Q

Glycogen is ……

A
  • similar structure ti amylopectin but more frequent branching (every 8 to 12 residues)
  • found in animal liver and muscle
  • also found in microbes
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55
Q

Why store glucose in polysaccharides?

A
  • Protects cells from high osmolarity
  • Glycogen in human liver
    • if hydrolyzed, it would form concentrated (0.4M) glucose solution and it would burst the cell
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56
Q

Fructan is …..

A

Fru (ß2–>6) Fru and Fru (ß2–>1) Fru
Found in plants
Slightly to highly soluble
Up to 30% of grass dry weight — good source of carbs for herbivores

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57
Q

What are examples of polysaccharides that are used in structural forms?

A

Cellulose, Hemicellulose, Pectin,ß- glucan, Chitin, Peptidoglycan, and Agarose

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58
Q

Cellulose have the following characteristics

A
  • Unbranched Glc(ß1–> 4)Glc
    —- identical to amylose, except the ß linkage
  • Tough, insoluble and indigestible
  • Found in cotton, plant cell wall (with other polysaccharides
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59
Q

What are the components of the plant cell wall?

A
  • cellulose
  • pectin
  • hemicellulose
  • ß- glucan
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60
Q

Hemicellulose has…..

A
  • Xylose core: Xyl(ß1–>4)Xyl
  • Branches that include arabinose and other sugars
    —- similar to glucose + branched heteropolysaccharide
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61
Q

Pectin has…….

A
  • Galacturonic acid core: GalA (∂1–>4) GalA
  • Branched that include arabinose, galactose and other sugars
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62
Q

ß-glucan……..

A
  • Glc(ß1–>4)Glc CORE with Glc(ß1–>3)Glc
  • Found in plants and microbes
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63
Q

Plant cell wall is

A
  • Indigestible by mammalian enzymes
  • Digested by Gastrointestinal microbes (bacteria in cows rumen) and some arthropods
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64
Q

Chitin

A
  • Unbranched N-acetylglucosamine: GlcNAc(ß1–>4) GlcNAc
  • found in exoskeletons of arthopods
  • second most abundant biomolecule on Earth (after cellulose)
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65
Q

Peptidoglycan

A
  • Unbranched N-acetylglucosamine and acetylmuramic acid: GlcNAc(ß1–>4) Mur2Ac
  • contains (crosslinked to) peptide side chain
    -found in cell wall of bacteria
  • broken down by lysozyme (in human tears = antibacterial)
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66
Q

Agarose

A
  • Make up of D- galactose and an L-galactose derivative
  • contains charged groups (sulfates and pyruvate)
  • red algae
  • used in gel electrophoresis
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67
Q

“Other” functional class of polysaccharides

A

glycosaminoglycans

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68
Q

What are Glycosaminoglycans?

A

-Polysaccharides from the extracellular matrix of animals
(extracellular matrix =space between cells)
- made of alternating acidic and amino sugars
- some contain charged groups (sulfates), forcing an extended configuration

Example: chondroitin sulfate

  • do not exist in free form
  • they are attached to proteins to form proteoglycans
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69
Q

Role of glycosaminoglycans in cells

A

Adhesion
Recognition
signaling

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70
Q

_____________ are covalently attached to glycoproteins

A

Oligosaccharides

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71
Q

Oligosaccharides are

A
  • rare, except when attached to proteins
  • Glycosylation = attachment
  • proteins forms are glycoproteins
    —> common in mammals = 50% of total proteins
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72
Q

What are glycoproteins?

A
  • oligosaccharides that are short and highly branched
  • acetylated residues (e.g., N-acetylglucosamine) common
  • Carbohydrate - protein linkages involves the following:

—> Sef/Thr or Asn on protein
—> O- or N- on oligosaccharide

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73
Q

Examples of glycoproteins

A

Mucin
- component of mucus
- hold water and form gels

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74
Q

Glycoproteins are recognized by

A
  • viruses
  • toxins
  • bacteria
  • other mammalian cells (leukocytes)

!!! important to virulence and immunity

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75
Q

Lipids are __________

A

structurally diverse

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76
Q

What the definition of a lipid

A
  • Biomolecules that are soluble in organic solvents.
    = ether, benzene, chloroform
  • no other shared feature
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77
Q

What are the two classifications of lipids

A
  • lipids that contain fatty acids
  • lipids that do not contain fatty acods
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78
Q

What are examples of lipids that DO have fatty acids?

A
  • Fatty acids
  • Triacylglycerols
  • Waxes
  • Membrane lipids
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79
Q

What are examples of lipids that DO NOT contain fatty acids?

A
  • Sterols
  • Fat soluble vitamins
  • Pigments
  • Polyketides
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80
Q

What is the major class of lipid?

A

Fatty acid

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81
Q

Fatty acid is made of?

A

Carboxylic acids with hydrocarbon chains between 4 to 36 carbons

  • Saturated = no double bonds
  • Unsaturated = one or more double bonds
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82
Q

Nomenclature (lipid number)

A
  • Palmitic acid
  • Oleic acid
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83
Q

Palmitic acid has (16:0)

A

(16:0) = 16 carbons with 0 double bonds

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84
Q

Oleic acid

A

(18:1 cis -9) = 18 carbons with 1 double bond in cis configuration beginning at carbon 9

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85
Q

Omega 3

A
  • double bond at 3rd carbon from end of the chain
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86
Q

how to write the lipid number

A
  • lipid number could be written as 18:3(n-3)
  • could also be written as 18:3 all cis-9,12,15
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87
Q

An example of an Omega 3 is required in the diet

A
  • ∂-linolenic acid
  • Eicosapentaenoic acid (EPA)
  • Docosahexaenoic acid (DHA)
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88
Q

∂- linolenic acid

A

cannot be synthesized
- animals lack desaturase enzymes to form the unsaturated bonds

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89
Q

Eicosapentaenoic acid (EPA) (20:5 n-3)

A
  • can be synthesized from ∂-linolenic acid to form the unsaturated bonds
  • otherwise required in diet
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90
Q

Docosahexaenoic acid (DHA) (22:6 n-3)

A

same as EPA

91
Q

What would happen if there is a deficiency in Omega 3

A

dermatitis, skin lesions, poor growth, reproductive failure

92
Q

Omega - 6

A
  • double bonds at 6th carbon from the end of the chain
93
Q

Examples of Omega-6 that are required in the diet

A
  • Linoleic acid
  • Arachidonic acid (AA) (20:4 n-6)
94
Q

Arachidonic acid (AA) (20:4 n-6)

A
  • if not enough linoleic acid available as a precursor
  • Always required in cats

Cats lack enzymes to synthesize from linoleic acid

95
Q

Where can Omega 3 and 6 be found

A

Fish oil

96
Q

Conjugated linoleic acid

A
  • Family of 28 isomers of linoleic acid
  • conjugated double bonds
    - alternating between single and double bonds
  • formed in rumen by microbes
    —- the process is known as biohydrogenation
97
Q

What is Cis configuraton

A

same side of double bond

98
Q

What is trans configuration

A

opposite side of the double bond

99
Q

Melting point

A
  • Decreases as the number of unsaturated bonds increases
  • Decreases as the chain length decreases
100
Q

Why does the melting point decrease as the number of unsaturated bonds increases?

A
  • This is especially for unsaturates bonds in cis configuration

—- the kinks prevents close packing of fatty acids

101
Q

_________________ store fatty acids

A

Triacylglycerols

102
Q

What is a Triacylglycerol?

A
  • ester of glycerol and fatty acids
  • it is the location of most fatty acids in cells
103
Q

Triacylglycerol is/are

A
  • Major form of energy storage in plants and in animals
  • Used over polysaccharides because of fatty acids
104
Q

Why are triacylglycerols used over polysaccharides ?

A

because fatty acids:

  • are more reduced carry more energy per carbon
  • are nonpolar and carry less water per gram
105
Q

________________ store fatty acids and repel water?

A

Waxes

106
Q

What are waxes

A
  • Ester of long-chain fatty acids with long-chain alcohols
  • Insoluble and have high melting points
107
Q

Functions of waxes

A

Storage of fatty acids in plankton
Protection and pliability for hair and skin in vertebrates
Waterproofing of feathers in birds
Protection from evaporation in plants
— useful as lotions, ointments, and polishes

108
Q

________ lipids that envelopes cells

A

Membrane Lipids

109
Q

Components of membrane lipids

A
  • phospholipids
  • glycolipids
  • archeal ether lipids
110
Q

Phospholipids

A
  • a similar structure to triacylglycerols
    – one fatty acid is substituted with the polar head group
  • Backbone may or may not be glycerol
  • Has a polar head group - contains phosphate and it may contain other constituents as well
111
Q

What is the backbone of glycerophospholipids?

A

Glycerol

112
Q

What is the backbone of sphingolipids?

A

Sphingosine

113
Q

What are the two phospholipids?

A
  • Phospohotidylcholine
  • Sphingomyelin
114
Q

Phospohotidiylcholine

A
  • glycerpphosophilid (glycerol back bone)
  • has a phosphocholine head group
  • one fatty acid = unsaturated
  • major membrane lipid for animals
  • absent in most bacteria - lack enzymes for synthesis
115
Q

Sphingomyelin

A
  • sphingolipid
  • like phosphotidylcholine, it has a phosphocholine head group
116
Q

Glycolipids have

A
  • similar structure to phospholipids but its polar head group is a carbohydrate NOT phophate
117
Q

Examples of a Glycolipid

A
  • Galactolipids
  • Glycosphingolipids
118
Q

What are Galactolipids?

A
  • Polar head group is one or two galactose residues
  • major membrane lipid in plants ( very important in plants)
119
Q

What are Glycophingolipids?

A
  • its polar head group is an oligosaccharide
  • it determines the blood type
    —> O antigen - Type O blood
    —> B antigen - type B blood
    —> A antigen - type A blood
  • Difference is only due to a single residue
    — A antigen has an extra N-acetylgalactosamine
    — B antigen has an extra galactose
120
Q

In glycosphingolipids, A antigen has an extra ________________.

A

extra N- acetylgalactosamine

121
Q

In glycosphingolipids, B antigen has an extra _________________.

A

extra galactose

122
Q

Archeal ether lipids

A
  • Found in archaea
  • have unusual structures
  • have Diphytanyl groups
123
Q

Why do Archaeal ether lipids have an unusual structure?

A
  • does not contain fatty acids –> hydrocarbons is instead diphytanyl
  • contains three glycerol residues ++ one is a head group and the other two are linked to the diphytanyl hydrocarbons
  • linkages are ether –> not amides or ester
124
Q

What is a Diphytanyl group?

A
  • Long (32 carbons) and span the entire membrane
    —— do not form lipid bilayer found in most organsims
125
Q

What are the reasons why Archaeal ether lipids have an unusual structure?

A
  • more stable under low pH and hot environments of some archaea
    —- ether linkage are more resistant to hydrolysis than ester
    —- the lipid “unilayer” they form is more stable than a bilayer
126
Q

Lipids

A

diverse biomolecules that only share one feature (solubility in organic solvents)

127
Q

Fatty acids are

A

Building block of many lipids

128
Q

Triacylglycerols, waxes, and membrane lipids differ in

A

structure and roles

129
Q

What are examples of lipids that do not contain fatty acids?

A
  • sterols
  • fat soluble vitamins
  • pigments
  • polyketides
130
Q

What lipid that does not contain a fatty acid contain a fused ring?

A

Sterols

131
Q

What is a steroid nucleus?

A

rings that make up structure

132
Q

Steroid nucleus has

A

3 rings with 6 carbons
1 ring with 5 carbons
structure is flat (planar) and rigid

133
Q

Sterols have

A

a polar head group (hydroxyl group) and nonpolar side chains (alkyl side chain)

134
Q

what are the types of sterols?

A
  • cholesterol
  • steroid hormones
  • bile acid
  • vitamin D precursor
135
Q

Cholesterol

A
  • most abundant sterol in animal tissue
  • component of cell membranes = controls fluidity in the membrane
  • can be obtained from the diet or synthesized in liver
  • transported in the blood via lipoproteins
136
Q

Lipoproteins include

A

HDL (good) and LDL (bad)

137
Q

Steroid hormones

A
  • Examples: estrogen and testosterone
  • do not contain an alkyl side chain = more polar than cholesterol
  • synthesized from cholesterol in gonads and adrenal glands
  • Carried through the body ain the bloodstream, usually attached to carrier proteins
  • many are sex hormones or reduce inflammation
138
Q

Other examples of sterols

A

testosterone, ß- estradiol, cortisol, prednisone, aldosterone, prednisolone, brassinolide

139
Q

What are bile acids?

A
  • Secreted by the gallbladder
  • emulsifiers (breaks up) fat droplets during digestion in small intestines
140
Q

Why do bile acids have to break down fat droplets?

A
  • fats need to be broken up so that enzymes can attack it
141
Q

What are fat soluble vitamins?

A
  • includes vitamins A,E,D & K
  • they have range of structures == the only shared feature is that they are fat soluble
142
Q

Vitamin D

A
  • sterol
  • precursor ( 7-dehydrocholesterol) synthesized from cholesterol
  • Synthesis of active form (calcitriol) is completed by
    - UV light in skin
    - Hydroxylation in liver and kidneys
143
Q

Where can Vitamin D be synthesized by

A

uv light
hydroxylation in liver and kidneys

144
Q

What are the functions of Vitamins D

A
  • Elevates plasma Ca ( and P)
    • Mechanism
      • stimulates intestinal absorption
      • bone resorption
      • Kidney tubular reabsorption
145
Q

What are the deficiency signs of Vitamin D?

A
  • skeletal deformities (rickets in children) + in adults weak bones
146
Q

Vitamin A has different forms

A

retinol (alcohol form)
ß- carotene ( 2 vitamin A molecules joined)
Others

147
Q

What are the functions of vitamin A?

A
  • normal night vision due to its role in formation of rhodopsin (pigment in rod photoreceptors of the eye)
  • hormone-like growth factor
148
Q

Deficiency signs of Vitamin A

A
  • poor night vision
149
Q

What vitamin is toxic in high amounts?

A

Vitamin A - don’t eat polar bear liver

150
Q

What is the structure of VItamin E?

A

most active form is ∂-tocopherol

151
Q

What are the functions of Vitamin E

A

free radical scavenger/ antioxidant

152
Q

What are the deficiency signs of vitamin E?

A

Nutritional muscular dystrophy ( weakness and awkward gait)

153
Q

What is the structure of Vitamin K

A

Major forms
K1 (phylloquinone) - plant
K2 (menaquinone) - animals
Synthetic form
K3 (menadione) - synthetic

154
Q

What are the functions of Vitamin K?

A
  • normal blood clotting
    —- involved in enzyme systems for the synthesis of prothrombin (factor II) and other clotting factors (IX, VII, X)
155
Q

What are the deficiency signs of Vitamin K?

A
  • prolonged clotting times, hemorrhage and death
156
Q

Vitamin K is illustrated in ___________

A

Rat poison - vitamin k antagonist — it kills rats because it interferes with the function of vitamin K

—- if they fall off the table and suffer from a small injury they will bleed to death

Heart disease patients get warfarin - low dose of rat poison – decreases blood clotting

157
Q

Natural pigments

A
  • have conjugated dienes = double bonds separated by a single bonds
158
Q

Natural pigments

A
  • pigments have conjugated dienes = double bonds separated by a single bond
159
Q

What are conjugated dienes?

A
  • excite by visible light and produce color
160
Q

____________ are secondary metabolites with medicinal uses

A

Polyketides

161
Q

What are polyketides?

A

lipids synthesized via reaction called Claisen reaction

162
Q

What is Claisen condensation reaction?

A
  • Same reaction used to synthesize fatty acids
  • lipids that are synthesized like fatty acids but are NOT fatty acids
163
Q

Polyketides are

A

secondary metabolites = metabolites are not essential to life but still beneficial
- medicinal properties

164
Q

Example of polyketide medical properties

A

Erythromycin (antibiotics)
Lovastatin (statin)
Amphotericin B (antifungal)

165
Q

Why are enzymes important?

A
  • Metabolism is impossible with enzymes
  • Enzymes are catalysts
  • They have high specificity
  • they can be regulated
  • they are effective under mild (physiological) conditions
166
Q

Enzymes are catalysts, what does this mean?

A

they speed up reactions to useful rates 10^5 vs 1

10^5 is faster than 1

167
Q

Enzymes have high specificity, what does this mean?

A

they carry out the reaction intended, not other, due to active site

168
Q

T/F: Most enzymes are proteins

A

TRUE

169
Q

When were enzymes first discovered?

A

late 1800s/ early 1900s

170
Q

What did Eduard Buchner do?

A

Yeast carry out fermentation even when cells are broken apart
- molecules (enzymes) inside yeast must be responsible
– vitalism is wrong

Zymase - breaking down cells

171
Q

What did James Sumner do?

A
  • he purified one enzyme (urease) and showed it was entirely protein
    -other investigators also showed other enzymes were protein
172
Q

How many amino acids per enzyme?

A

around 100 to 10,000

173
Q

Since enzymes also have cofactors, what do cofactors mean?

A

non-amino acids molecules required for activity

174
Q

What are the types of cofactors?

A

Inorganic ions and Organic molecule

175
Q

What are the inorganic ions?

A

Fe 2+ (iron)
Mg 2+ (magnesium)
Mn 2+ (manganese)
Zn 2+ (zinc)

176
Q

What are the organic molecules (coenzymes)

A
  • mostly vitamins
  • carry functional groups during reactions
177
Q

what is a holoenzyme?

A

Enzyme + cofactor

178
Q

What is an Apoenzyme?

A

Enzyme alone

179
Q

What are Ribozymes?

A
  • involved in gene expression
180
Q

example of a ribozyme?

A

rRNA= Ribosomal RNA

= catalyzes the synthesis of protein

181
Q

How are enzymes classified?

A

by the reactions they catalyze

182
Q

when there are only a few enzymes known naming was easy

A

like urease

183
Q

Things got more difficult as more enzymes were discovered (21 enzymes were urea

A

sol: classify and name enzymes by the reactions they catalyze

Example: hydrolase

urea is now named urea amidohydrolase

184
Q

What does hydrolase do?

A

Carry out hydrolysis reaction

185
Q

What are the 7 classes in classifying enzymes?

A
  1. Oxidoreductases - transfer electrons
  2. Transferase - group transfer reactions
  3. Hydrolases - hydrolysis reactions
  4. Lyase -
  5. Isomerase
  6. Ligase
  7. Translocases
186
Q

EC means

A

Enzyme commission number - unqiue number ID for enzymes

187
Q

What is the first number in EC. 3.5.1.5 indicate?

A

3 is the class number

188
Q

What is the last three numbers in EC. 3.5.1.5 indicate?

A

5.1.5 are the Subclasses

189
Q

_________ affect reaction rate, not direction

A

Enzymes

190
Q

How do catalysts increase rate of reaction?

A
  • lowering activation energy (∆G dagger)
  • they cannot change the total energy released (∆G)
    —- they do not make unfavorable reactions more favorable
191
Q

How does enzymes start a reaction?

A

Enzymes bind to substrates to start reaction and they continue to bind as substrates transformed into products

192
Q

Where does binding happen?

A

All binding occurs in active site
—> has amino acids complementary to substrates, intermediates and product
- this gives enzymes their specificity

193
Q

What does binding do?

A

Lowers activation energy –> faster reaction rate

194
Q

Transition state

A

is even more important than binding to a substrate

195
Q

How can you tell when a reaction can proceed?

A
  • bringing substrates to the transition state
196
Q

Why is it important to lower the activation energy is there are multiple substrates?

A

It brings them closer proximity

197
Q

What are the specific catalytic groups that contribute to catalysis?

A
  1. Acid-base
  2. Covalent
  3. Metal ion
198
Q

what does acid-base catalysis do?

A

proton transferred from enzyme to reactants and vice versa

199
Q

What does Covalent Catalysis do?

A
  • transient covalent bond formed between enzyme and substrate
  • changes the reaction pathway
    • uncatalyzed A-B –> A+B
      catalyzed (X: = nucleophile catalyst) A-B+X: –> -X+B—> A+B + X:
  • requires a nucleophile (X:) on the enzyme

Example: neg charged oxygen (O-) that can form on serine

200
Q

Metal Catalysis

A
  • involves a mnetal ion bound to the enzyme
  • interacts with substrate to facilitate binding
    • stabilizes negative charges
  • participates in oxidation reactions
201
Q

Chymotrypsin

A

breaks down dietary proteins to peptises during digestion
uses both acid-base catalysis + covalent catalysis

202
Q

Step 1: substrate enters

A
  • peptide enters and is bound to the enzyme ( at the hydrophobic pocket)
203
Q

step 2: Colavent catalysis

A

Enzyme (Ser 195) forms covalent bonds with peptide (at carbonyl group)
- enzyme (His 57 and Gly 193 ) stabilize transition state by hydrogen bonding to peptide

204
Q

step 3 Acid base catalysis

A
  • Enzyme (His57) donates proton to peptide
  • Protonation cleaves peptide bond
  • Product 1 (shortened peptide) leaves
205
Q

step 4 water enters

A

water enters enzyme active site

206
Q

step 5 cont acid base catalysis

A
  • Water donates a proton to enzyme (His57) to replace proton at step 3
  • hydroxyl is leftover and this attacks enzyme-substrate complex (ester linkage)
207
Q

step 6 cont covalent catalysis

A

covalent bond between peptide and enzyme (ser 195) is broken

208
Q

step 7 product 2 leaves

A
  • Product 2 (the shortened peptide) is replaced
  • Free enzyme is regenerated
209
Q

Enolase

A
  • removes water during glycolysis
  • uses acid-base and metal catalysis
210
Q

Step 1 acid base and metal catalysis

A
  • Substrate (2-phosphoglycerate) enters
  • Enzyme (Lys345) accepts proton
  • Metal ion (Mg2+) stabilizes intermediat
211
Q

step 2 Acid base and metal catalysis cont

A
  • Metal ion (Mg2+) continues to stabilize intermediate
  • Enzyme (Glu211) donates proton to intermediate
  • Product (phosphoenolpyruvate) and water leave
212
Q

What are the factors that affect the rates of enzymatic reactions?

A
  • enzyme concentration
  • substrate concentration
  • Modulators and concentration
  • temperature
  • pH
213
Q

What is the study of reactions and the factors affecting them called?

A

Enzyme kinetics

214
Q

What is the most important part in doing experiments when determining the rate of reaction?

A

Initial rate

215
Q

Why is the initial rate important?

A

The substrate is still at concentration added by the experimenter.

216
Q

What is the relationship between initial rate and concentration called?

A

Michaelis- Menten Kinetics

217
Q

What are the two parameters in Michaelis-Menten kinetics?

A

V max = maximal rate of reaction
Km = substrate concentration at 1/2 Vmax

218
Q

What is the simple equation in michaelis menten kinetics?

A

v = (Vmax [S]) / (km+ [S])

219
Q

what is Vmax?

A

unit is mol L^-1 s^-1
higher value = faster the rate

220
Q

Under Vmax, what is the enzyme concentration is known (kcat)?

A

Kcat = Vmax/ [E]

221
Q

Why is Kcat better than Vmax?

A

it accounts for different concentrations of enzymes across experiments

222
Q

What is the unit for kcat?

A

s^-1

223
Q

Km

A

units: mol L^-1
higher value, the slower rate
Does not affect the rate of substrate concentration is very high (v = V max)

ABI 102 WINTER QTR (4 decks)

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